lua could actually be quite simple:
sed -i.bak 's/disable_lua.*/disable_lua = true/g' /path/to/luafile
Would create the backup. You'd just have to nut out the sed command properly.

I have a request/thought/suggestion: perhaps a "purge all programs and start them fresh" option to the program. That way instead of having people who don't quite know what they're up to asking how to clean and remove etc. you could rm/deinstall the program directories and start them from scratch.